GgaALTA1009008-2/2 @ galGal4
Alternative 3'ss
Gene
ENSGALG00000026836 | COL16A1
Description
collagen, type XVI, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2193]
Coordinates
chr23:4930803-4931029:-
Coord C1 exon
chr23:4930940-4931029
Coord A exon
chr23:4930848-4930850
Coord C2 exon
chr23:4930803-4930847
Length
3 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGT
5' ss Score
10.1
3' ss Seq
TGACCGCGTGTGCTGATCAGCAG
3' ss Score
2.41
Exon sequences
Seq C1 exon
GGGGACTCCTGCCTGTCCTGTGACAGCCGTGTCCTCGCTGCGCTGCTGCGGGAACTCCCCGAGGGGCGTGAGAGCGAACTGGGATCACTG
Seq A exon
CAG
Seq C2 exon
GACAAAGCAATCCTTCCTGGGCTGGCTGGCATCAAGGGCGAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000026836-30-32,30-31-2/2
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (No Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.567 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(8.7=13.3),PF0139113=Collagen=PU(3.0=6.7)
A:
NA
C2:
PF0139113=Collagen=FE(21.2=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACTCCTGCCTGTCCTGTGAC
R:
GCCCAGGAAGGATTGCTTTGT
Band lengths:
108-111
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]